id stringlengths 36 36 | text stringlengths 1 1.25M |
|---|---|
7063657b-6705-4884-a155-e04de1821df2 | public void setEffReadLength(int effReadLength) {
this.effReadLength = effReadLength;
} |
9d39fab9-9d3f-4dcc-984a-542fce8c8395 | public ReferenceReadPosition(byte[] nucleotidesInReference,
byte[] affectedRefAllel, int indexOfRefAllele) {
this.setNucleotideInReference(nucleotidesInReference);
if (affectedRefAllel.length == 1) {
this.refAllel = (char) affectedRefAllel[0];
}
this.indexOfRefAllele = indexOfRefAllele;
} |
46f421d1-6248-497a-b4ac-cbedc05b55d8 | public static ReferenceReadPosition getReferenceReadPositionInstance(
String string, int posInContig, int flankingRevBp, int flankingForBp) {
ReferenceSequence rf = CheKov.getIndexedFastaSequenceFile_Ref()
.getSubsequenceAt(string, posInContig - flankingRevBp,
posInContig + flankingForBp);
// the cons... |
e7467289-681f-4f7f-afb0-b4302af435a0 | public byte[] getNucleotideInReference() {
return nucleotidesInReference;
} |
b738468e-9f3c-4d25-b558-7297e322fb0e | public void setNucleotideInReference(byte[] nucleotideInReference) {
this.nucleotidesInReference = nucleotideInReference;
} |
7cf93ca2-3ff7-48f1-b43e-0802e99c95d5 | @Override
public String toString() {
String s = "";
for (byte b : nucleotidesInReference) {
s = s + String.format("%c", b);
}
return "[" + s + "]";
} |
2e90def5-9158-46a0-ad06-e349bad3dc4b | public char getRefAllel() {
return refAllel;
} |
fcf29232-b796-46b6-8865-3c63d0006722 | public void setRefAllel(char refAllel) {
this.refAllel = refAllel;
} |
0f64d284-5050-4360-a562-c598ae09f209 | public int getIndexOfRefAllele() {
return indexOfRefAllele;
} |
e10e8efb-5ec9-453b-ac6a-7853985a41b4 | public void setIndexOfRefAllele(int indexOfRefAllele) {
this.indexOfRefAllele = indexOfRefAllele;
} |
e44beecc-1aae-4c03-b10f-8c1672896ccb | public static void main(String[] args) {
try {
IndexedFastaSequenceFile ifsf = new IndexedFastaSequenceFile(
new File(
"/home/dboehm/NewReference_2012_06_24/share/reference/genomes/NCBI_GRCh37/NCBI_GRCh37.fa"));
System.out.println(ifsf.isIndexed());
ReferenceSequence rs = ifsf.getSequence("chr1")... |
3a65be91-f653-4625-af9c-caf37ed82a81 | Node(IntervalAbs newData) {
left = null;
right = null;
data = newData;
} |
6af5a029-918f-4da9-ad6d-9e99b9c0e340 | public BinaryTreeIntervalHelper() {
root = null;
} |
03bc6b6e-1caa-417f-b02b-593ce42159d8 | public boolean lookup(IntervalAbs data) {
return (lookup(root, data));
} |
4e33f170-7012-41fc-81bd-3dddfffb9e6a | private boolean lookup(Node node, IntervalAbs data) {
if (node == null) {
return (false);
}
if (data == node.data) {
return (true);
} else if (data.getStartAbs() < node.data.getStartAbs()) {
return (lookup(node.left, data));
} else {
return (lookup(node.right, data));
}
} |
e698c90c-6824-41d3-839e-cc20c2e5cd4e | public void insert(IntervalAbs data) {
root = insert(root, data);
} |
4cdf746b-1d53-4aa1-a1f8-c21c49ba8899 | private Node insert(Node node, IntervalAbs data) {
if (node == null) {
node = new Node(data);
} else {
if (data.getStartAbs() <= node.data.getStartAbs()) {
node.left = insert(node.left, data);
} else {
node.right = insert(node.right, data);
}
}
return (node); // in any case, return the new ... |
099a4231-f356-4e8f-aa6e-0e27c56670fb | public int size() {
return (size(root));
} |
14a69770-f620-4af4-8d3d-a7d123410e91 | private int size(Node node) {
if (node == null)
return 0;
else
return (size(node.left) + 1 + size(node.right));
} |
746596fe-e343-4975-9fec-34cca910cafe | public int maxDepth() {
return (maxDepth(root));
} |
38643cbd-03e8-4af3-9b39-f3fe337a0a90 | private int maxDepth(Node node) {
if (node == null)
return 0;
else {
int lDepth = maxDepth(node.left);
int rDepth = maxDepth(node.right);
// use the larger + 1
return (Math.max(lDepth, rDepth) + 1);
}
} |
2147aba7-70aa-45bc-9348-8607b16055c2 | public IntervalAbs minValue() {
return (minValue(root));
} |
c001ce02-2be8-410b-af30-b38a73a77059 | private IntervalAbs minValue(Node node) {
Node current = node;
while (current.left != null)
current = current.left;
return current.data;
} |
8c45720a-9248-4d3e-9230-5b0538533735 | public IntervalAbs maxValue() {
return (maxValue(root));
} |
f813a712-bad9-4743-a165-350e1327ebe4 | private IntervalAbs maxValue(Node node) {
Node current = node;
while (current.right != null)
current = current.right;
return current.data;
} |
9ba32b60-f84a-4533-9516-d30cee51b099 | public void printTree() {
printTree(root);
System.out.println();
} |
1cc9286e-7d19-4ae4-912f-7bc6796567df | private void printTree(Node node) {
if (node == null)
return;
// left, node itself, right
printTree(node.left);
System.out.print(node.data + " ");
printTree(node.right);
} |
67725112-3b89-440e-9823-a8f0d4278633 | public void printPostorder() {
printPostorder(root);
System.out.println();
} |
24f48924-f612-4296-8ee5-c78779cbc441 | public void printPostorder(Node node) {
if (node == null)
return;
// first recur on both subtrees
printPostorder(node.left);
printPostorder(node.right);
// then deal with the node
System.out.print(node.data + " ");
} |
1f81158d-5aed-4f06-858a-bb1c0247f101 | public void printPaths() {
long[] path = new long[1000000];
printPaths(root, path, 0);
// for (int i : path)
// System.out.println(i);
} |
e1b3c0b6-165a-458d-b60e-8f9c977dde21 | private void printPaths(Node node, long[] path, int pathLen) {
if (node == null)
return;
path[pathLen] = node.data.getStartAbs();
pathLen++;
// it's a leaf, so print the path that led to here. It is a leaf, if
// node.left AND node.roght = NULL
if (node.left == null && node.right == null) {
for (int i... |
b992e295-bb86-45d4-90ab-d93e6a289e47 | public void mirror() {
mirror(root);
} |
bb7ed9c2-7621-4ba6-9aeb-081b38cab1ea | private void mirror(Node node) {
if (node != null) {
// do the sub-trees
mirror(node.left);
mirror(node.right);
Node temp = node.left;
node.left = node.right;
node.right = temp;
}
} |
c1808cc3-8fbc-4d11-9177-31d5254f7d2e | public void printInOrder(Node node) {
if (node != null) {
printInOrder(node.left);
System.out.println(" Traversed " + node.data);
printInOrder(node.right);
}
} |
f3b20a8e-5df5-4ad6-8605-e94fa0325753 | public static void main(String[] args) {
try (BufferedReader br = new BufferedReader(new FileReader(args[0]))) {
String line;
while ((line = br.readLine()) != null) {
String[] lineFields = line.split("\t");
createAnnotationSet(lineFields[0]);
Annovar_GATK_SNV_Entry annovarGATKSNV_Entry = new Annova... |
fb70085c-154a-43c8-a617-adc44cf24b8e | private static void createAnnotationSet(String s) {
AnnovarAnnotation newAnno = new AnnovarAnnotation(s);
if (!annotationEntries.contains(newAnno)) {
annotationEntries.add(newAnno);
} else {
for (AnnovarAnnotation anno : annotationEntries) {
if (anno.equals(newAnno)) {
anno.setCount(anno.getCount()... |
fc6e97b2-b0a7-4e79-ae36-4e39082ae65c | public static void main(String[] args) {
CheKov.setStartTime(Math.abs(System.nanoTime()));
String bedfile = args[0];
String bamfile = args[1];
String outfile = args[2];
String missedBEDFile = args[3];
// we need to do IMPORTANTLY some useful things with this parameter
IntervalAbs.INTERVAL_THRESHOLD = Inte... |
9a403313-1b72-4430-82a8-bd3711a250ba | public static void printQCResult() {
System.out.printf("%-35s%,12d%n%-35s%,12d%n%-35s%,12d%n",
"All Reads: ", ReadEntry.getReadCount(), "FragmentReads:",
FragmentReadEntry.getFragmentReadCount(), "PairedReads:",
PairedReadEntry.getPairedEndReadCount());
System.out.printf("%-35s%,12d%n%-35s%,12d%n", "OnT... |
d4b003b0-e17f-4e8d-bdb4-88753dab8d45 | public static int medianFromArray(int[] array) {
int counter = ReadEntry.getReadCount();
for (int i = 0; i < 2000; i++) {
counter = counter - array[i];
if (counter <= (int) ReadEntry.getReadCount() / 2) {
return i;
}
}
return 0;
} |
8705c515-fefa-459f-adce-a2eac6794dbb | public static TreeSet<IntervalAbs> getIntervalTreeSet() {
return intervalTreeSet;
} |
445883e6-6946-4a06-a861-973eb662a0bd | public static void setIntervalTreeSet(TreeSet<IntervalAbs> intervalTreeSet) {
CheKov.intervalTreeSet = intervalTreeSet;
} |
be5b5595-13b1-4807-a273-2d3e2126e1e8 | public static long getAllBases() {
return allBases;
} |
7474a138-6ff1-4117-aa52-33b29b71c3a5 | public static void setAllBases(long allBases) {
CheKov.allBases = allBases;
} |
189ce9a1-f31d-4fc2-baa9-5246d0d03cc8 | public static long getAllHardClippedBases() {
return allHardClippedBases;
} |
b5417dca-9ae8-45c5-b6d9-d117efec9417 | public static void setAllHardClippedBases(long allHardClippedBases) {
CheKov.allHardClippedBases = allHardClippedBases;
} |
80a9033e-2e2a-45e1-9fd5-284e5acca2b7 | public static long getAllSoftClippedBases() {
return allSoftClippedBases;
} |
cf5c259e-8650-4007-ba34-1d45f3604c1e | public static void setAllSoftClippedBases(long allSoftClippedBases) {
CheKov.allSoftClippedBases = allSoftClippedBases;
} |
69874884-d04d-4a7b-95cb-99d907000d37 | public static long getAllDeletedTaggedBases() {
return allDeletedTaggedBases;
} |
61be066a-604e-46d4-9abb-89864da4d7d8 | public static void setAllDeletedTaggedBases(long allDeletedTaggedBases) {
CheKov.allDeletedTaggedBases = allDeletedTaggedBases;
} |
2a945dfc-ef3a-4671-a793-1dca95206721 | public static long getAllInsertedTaggedBases() {
return allInsertedTaggedBases;
} |
48c08cdf-887e-4679-b585-56e18dc1d74e | public static void setAllInsertedTaggedBases(long allInsertedTaggedBases) {
CheKov.allInsertedTaggedBases = allInsertedTaggedBases;
} |
918a85b7-9233-4bbd-967e-788ce1dc0b2c | public static long getAllDeletedTaggedReads() {
return allDeletedTaggedReads;
} |
faec46a9-1d87-4b66-8544-dcf45353bc2d | public static void setAllDeletedTaggedReads(long allDeletedTaggedReads) {
CheKov.allDeletedTaggedReads = allDeletedTaggedReads;
} |
8165167a-4822-4639-b7f9-66398ac4bfa2 | public static long getAllInsertedTaggedReads() {
return allInsertedTaggedReads;
} |
17c3edde-9f9e-4350-8f93-a663e8148068 | public static void setAllInsertedTaggedReads(long allInsertedTaggedReads) {
CheKov.allInsertedTaggedReads = allInsertedTaggedReads;
} |
350b1a3a-dfe7-408d-92a8-05b98601188c | public static long getAllEitherDeletedOrInsertedTaggedReads() {
return allEitherDeletedOrInsertedTaggedReads;
} |
07944a9b-b76a-4955-93a4-de6e942f01dc | public static void setAllEitherDeletedOrInsertedTaggedReads(
long allEitherDeletedOrInsertedTaggedReads) {
CheKov.allEitherDeletedOrInsertedTaggedReads = allEitherDeletedOrInsertedTaggedReads;
} |
c4064fd1-65aa-431b-b1e1-29123baec263 | public static long getMedianEffReadLength() {
return medianEffReadLength;
} |
3fa7fb64-a640-48df-9e0b-d831a2cfe67d | public static void setMedianEffReadLength(long medianEffReadLength) {
CheKov.medianEffReadLength = medianEffReadLength;
} |
9cdd68c0-661e-459e-b2cd-04b462d1e378 | public static long getMedianRawReadLength() {
return medianRawReadLength;
} |
4db727ad-3ed1-43ad-9e1b-a6e64facc60c | public static void setMedianRawReadLength(long medianRawReadLength) {
CheKov.medianRawReadLength = medianRawReadLength;
} |
e75f7f2f-8a86-498a-9ff0-2b6ccd9244ad | public static long getAvEffReadLength() {
return avEffReadLength;
} |
ada0fb63-9143-4f08-96b3-391c8b6d9da0 | public static void setAvEffReadLength(long avEffReadLength) {
CheKov.avEffReadLength = avEffReadLength;
} |
598c564f-e9d9-41be-8142-6339b094300b | public static long getAvRawReadLength() {
return avRawReadLength;
} |
64561811-0006-4ace-854b-f8e0c2dc4568 | public static void setAvRawReadLength(long avRawReadLength) {
CheKov.avRawReadLength = avRawReadLength;
} |
6792a51a-381f-4e47-88ab-ebba809b61f3 | public static TreeSet<TargetNucleotidePositionEntry> getAlteredNucleotidePositionsEntries() {
return alteredNucleotidePositionsEntries;
} |
5c7cc631-40d7-4f9a-9c2a-6a16d804b650 | public static void setAlteredNucleotidePositionsEntries(
TreeSet<TargetNucleotidePositionEntry> alteredNucleotidePositionsEntries) {
CheKov.alteredNucleotidePositionsEntries = alteredNucleotidePositionsEntries;
} |
010ecaf6-8c70-4df4-a9c1-c180bebfa9c1 | public static long getStartTime() {
return startTime;
} |
f55e1f50-7b39-4f34-be09-41e887b1487f | public static void setStartTime(long startTime) {
CheKov.startTime = startTime;
} |
363778b6-7096-4dc2-b6a3-652d18b619c6 | public static long getEndTime() {
return endTime;
} |
c27a3646-a3de-463c-b484-afec5c8f5c22 | public static void setEndTime(long endTime) {
CheKov.endTime = endTime;
} |
25d1eb6f-3385-449c-b650-05454a49198e | public static IndexedFastaSequenceFile getIndexedFastaSequenceFile_Ref() {
return indexedFastaSequenceFile_Ref;
} |
473754ef-5bee-4e57-a032-def6197cc90e | public static void setIndexedFastaSequenceFile_Ref(
IndexedFastaSequenceFile indexedFastaSequenceFile_Ref) {
CheKov.indexedFastaSequenceFile_Ref = indexedFastaSequenceFile_Ref;
} |
dae3bc29-efeb-43de-844c-4342a5219c34 | public Annovar_GATK_SNV_Entry(String annotationType, String gene,
GATK_SNV_entry gatk_SNV_entry) {
// this seems to be redundant, but at the moment necessary because of
// the missing super() constructor. Needs to be addressed
super(gatk_SNV_entry.getChr(), gatk_SNV_entry.getGenomPosition(),
gatk_SNV_entry... |
3464db4b-946e-40e1-986c-e5988e373eb9 | public String getAnnotationType() {
return annotationType;
} |
8f6c3258-78bd-4946-a887-4607202ff3d1 | public void setAnnotationType(String annotationType) {
this.annotationType = annotationType;
} |
c9223a9f-5ee2-45f4-8797-f3e17335b199 | public String getGene() {
return gene;
} |
f95529f9-a550-487e-8e71-caa6335fed35 | public void setGene(String gene) {
this.gene = gene;
} |
203f3c2b-8057-4754-b478-54046a6d8045 | public GATK_SNV_entry getGatk_SNV_entry() {
return gatk_SNV_entry;
} |
4be286ac-d8fc-46fd-8cec-c9b8a990609a | public void setGatk_SNV_entry(GATK_SNV_entry gatk_SNV_entry) {
this.gatk_SNV_entry = gatk_SNV_entry;
} |
f35f8392-1bf2-4624-a7d6-25165ef5dfbc | public AnnovarAnnotation(String annotation) {
this.setAnnotation(annotation);
this.count = 1;
} |
81e2e4ed-e5a6-4a60-a01e-8704268bb087 | public String getAnnotation() {
return annotation;
} |
55f873b8-bb64-4e0d-a42f-5c327351b821 | public void setAnnotation(String annotation) {
this.annotation = annotation;
} |
fa3fa416-ed29-45c7-8426-db48bad0bcb4 | public Integer getCount() {
return count;
} |
6a91d380-f043-45f4-ad08-9f23f21d969f | public void setCount(Integer count) {
this.count = count;
} |
aa6ffd9a-6f33-47dc-82b8-4dc590b659cf | @Override
public boolean equals(Object obj) {
if (obj == null)
return false;
if (obj == this)
return true;
if (!(obj instanceof AnnovarAnnotation))
return false;
AnnovarAnnotation that = (AnnovarAnnotation) obj;
return (that.annotation.equals(this.annotation));
} |
a7f8bf9a-8f2c-40c7-b1a8-5cc95dffaf51 | @Override
public int compareTo(Object obj) {
AnnovarAnnotation that = (AnnovarAnnotation) obj;
return this.annotation.compareTo(that.annotation);
} |
9533f31e-99c5-49c6-94dd-2b437c36b68c | public ObjectDDL(String objectName, String objectDDL, String schema, String type) {
_objectName = objectName;
String s = Character.toString((char) 10);
String sFrom = s+s;
_objectDDL = objectDDL.replaceAll(sFrom, s).trim();
// Terminatore per oggetti codice
if (type=="FUNCTION" | type=="PROCEDUR... |
f6f8ba6e-e5e7-41ee-9aff-254527bca939 | public String Elabora(String outputFolder, String subf) {
System.out.println("Estrazione ddl per l'oggetto ["+_objectName+"]");
String fileName = _type+"."+_objectName+".sql";
try {
FileWriter fstream = new FileWriter(outputFolder+"/"+subf+"/"+fileName);
BufferedWriter out = new BufferedWriter(fstr... |
8d7df323-2702-43d9-8b5c-0c9fba226a7f | public DbObjectType() {
} |
53d2e20d-34a0-46a5-ba2c-61de95bcbb5c | public DbObjectType(Connection c, String schema) {
this._conn = c;
this._schema = schema;
this._mapSql = new HashMap<String, String>();
/*
_hmSql.put("TABLE", "select object_name, DBMS_METADATA.GET_DDL('TABLE',object_name) from user_objects where object_type = 'TABLE' and generated = 'N'");
_hmSq... |
2fc33238-830b-46e3-9320-9bc6fef2edbf | public ObjectDDLContainer ExtractDDL(String type) {
System.out.println("Estrazione oggetti di tipo. ["+type+"].");
Clob lobValue;
ObjectDDLContainer a = new ObjectDDLContainer(type, _schema);
try {
Statement stmt = _conn.createStatement();
ResultSet rs = stmt.executeQuery(_mapSql.get(ty... |
5f0a4c05-412e-4e29-bfc0-35550b03c540 | public static String getTerminator() {
return _terminator;
} |
77492a96-8a6c-4b65-a76e-67dcfe13ed49 | public static void main(String[] args) {
// TODO Auto-generated method stub
//String a = System.getProperty("line.separator");
//System.out.println(a);
String s = Character.toString((char) 13)+Character.toString((char) 10);
_terminator = s;
/*args = new String[4];
args[0] = "-username=suetl01"... |
6332d83c-1cb0-4c04-a192-61c0e551be99 | private static String getArgs(String[] args, String name) {
String[] values;
for (int i=0;i<args.length;i++) {
//System.out.println(args[i]+'\n');
if (args[i].indexOf("-"+name)!=-1) {
values = args[i].split("=");
//System.out.println(values[1]+'\n');
return values[1];
}
}
r... |
06b3072b-2739-46f8-b3cc-4bc07f47e68e | private static boolean getArgsB(String[] args, String name) {
String[] values;
for (int i=0;i<args.length;i++) {
//System.out.println(args[i]+'\n');
if (args[i].indexOf("-"+name)!=-1) {
values = args[i].split("=");
//System.out.println(values[1]+'\n');
if (values[1]=="false")
re... |
132afd74-75a5-464f-b1a9-2645c6ecb4c7 | public DDLConnection(String cs, String outputFolder, String userName, String password, boolean withTables, String outputObjs, String outputCode) {
try {
System.out.println("Connessione al db oracle.");
DriverManager.registerDriver (new oracle.jdbc.driver.OracleDriver());
_conn = DriverManager.getConnectio... |
e3739819-1ba8-4fc4-bb99-5daf9ad5cbf9 | public void close() {
try {
_conn.close();
}
catch (SQLException se) {
System.out.println(se.getMessage());
System.out.println(se.getStackTrace().toString());
}
} |
df9bae28-31b6-466d-a416-c646a9fc3b42 | public void writeLine(String type, DbObjectType o, BufferedWriter out, String sort, String subf) {
String line;
try {
line = o.ExtractDDL(type).elaboraFile(_outputFolder, sort, subf);
if (line!="")
out.write("@"+line+DDLExtractor.getTerminator());
}
catch (IOException ioe) {
System.out... |
106be93d-340b-453a-80e2-fc58df9a5317 | public void ExtractDDL() {
DbObjectType o = new DbObjectType(_conn, _schema);
// Creazione del file master
String fileName = _outputFolder+"/01.main.sql";
try {
System.out.println("Inizio elaborazione oggetti.");
FileWriter fstream = new FileWriter(fileName);
BufferedWriter out = new B... |
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